Nine months later, though, Egypt’s freethinkers and religious minorities are still waiting for the new leadership to deliver on that promise. Having suppressed Mr. Morsi’s Islamist supporters, the new military-backed government has fallen back into patterns of sectarianism that have prevailed here for decades.

Prosecutors continue to jail Coptic Christians, Shiite Muslims and atheists on charges of contempt of religion. A panel of Muslim scholars has cited authority granted under the new military-backed Constitution to block screenings of the Hollywood blockbuster “Noah” because it violates an Islamic prohibition against depictions of the prophets.

The military leader behind the takeover, Abdul-Fattah el-Sisi, often appeals to the Muslim majority in a language of shared piety that recalls Anwar el-Sadat, nicknamed the believer president, who invoked religious authority to bolster his legitimacy and inscribed into the Constitution the principles of Islamic law.

Mr. Sisi has listened attentively as Muslim clerics allied with him have offered religious justifications for violence against his Islamist opponents. A prominent Muslim scholar compared him and his security chief to Moses and Aaron. The new government has tightened its grip on mosques, pushing imams to follow state-approved sermons.

Many Coptic Christians and other religious minorities cheered the military takeover because they feared the Muslim Brotherhood, a religiously exclusive movement whose leaders have a history of denigrating non-Muslims. The military authorities shut down ultraconservative Islamist satellite networks that had stigmatized Christians or Shiite Muslims. And the military sponsored constitutional revisions that scaled back the references to Islamic traditions and declared with new directness that religious freedom was now absolute.

In some ways, however, sectarian tensions have worsened: Coptic Christians, who make up about 10 percent of the population, have faced violence and scapegoating from Islamists angry about the church’s support for the takeover. Prosecutors and police officers — almost all in their jobs long before Mr. Morsi took office — have done little to protect the Christians or other religious minorities, rights advocates say.

“Nothing has really changed,” said Kameel Kamel, a Coptic Christian in Asyut whose son Bishoy, 26, was jailed under Mr. Morsi on charges of posting blasphemy on Facebook.

Mr. Kamel hoped that the end of Islamist rule would free his son, and last November the family was elated when an appeals court ordered a retrial.

But five months later, his son is still behind bars. Perhaps fearful of the mob that gathered outside court for the younger Mr. Kamel’s first hearing, the prosecutors have ignored court deadlines for his release or retrial. “My hopes were disappointed,” the father said. Prosecutors declined to comment.

Despite its sweeping language, the revised Constitution still limits religious freedom to Muslims, Christians and Jews. It also stipulates that Parliament should regulate crimes like contempt of religion.

Christians and religious dissenters may “feel better psychologically” because the Islamists have been pushed underground, said Ishak Ibrahim, a researcher at the Egyptian Initiative for Personal Rights. But the “culture of sectarianism” persists in practice, he said.

The dispute over “Noah,” a film about the epic flood common to the Bible and the Quran, is a high-profile test. Early last month, a panel of Muslim scholars issued a statement about the film that began by pointing out that the revised Constitution not only continues to incorporate the principles of Islamic law, but also makes their institute, Al Azhar, the exclusive authority on interpreting Islam.

“Noah,” the scholars declared, is “religiously prohibited” as “a clear violation of the principles of Islamic Shariah.”

The culture minister fired back that the decision was up to the censorship board. But it has not yet authorized the film, and this month the board and the Culture Ministry declined to comment.

In 2012, Karam Saber, the author of a short-story collection, “Where Is God?” was sentenced in absentia to five years in prison for blasphemy, after complaints by ultraconservative sheikhs in the city of Beni Suef.

But after the military takeover, an appeals court solicited a review of the book by a committee of Azhar scholars. Last month, the court upheld the sentence.

In the Suez Canal city of Ismailia, prosecutors have detained a student, Sherif Gaber, since last fall on allegations that he started a Facebook page for atheists. When open atheism in Alexandria was discussed on a talk show, the city’s security chief promised to crack down there.

Shiite Muslims — considered heretics by many in Egypt’s Sunni Muslim majority — have also been a target “in the hunting of religious minorities,” said Mr. Ibrahim of the Egyptian Initiative for Personal Rights. One was arrested while trying to visit the landmark Hussein Mosque on a Shiite holy day. Convicted of blasphemy, he was sentenced to five years in prison. The police are now holding two more Shiites in detention in the northern province of Dakahleya, where they are under investigation for similar charges, Mr. Ibrahim said.

Mr. Sisi, a former general who stepped down to run for president, often portrays himself as the champion of a benign understanding of Islam, accusing his Islamist opponents of twisting the faith.

“Islam has never been like this,” Mr. Sisi said while addressing his fellow Muslims in a televised speech in August. “It has never scared anybody or terrified anybody, regardless of whether the person it is addressing is good or bad.”

But the clerics closest to Mr. Sisi can be harsh toward those they deem bad Muslims.

Last month, for example, state television cameras followed Mr. Sisi to a military installation for a Friday Prayer service led by Sheikh Ali Gomaa, a former mufti and a close Sisi ally. During the broadcast, Sheikh Gomaa referred indirectly but unmistakably to Mr. Sisi’s Islamist opponents as a “faction of hypocrites” who were “plotting schemes against the Muslims.” He lauded the soldiers and police officers who fought such “terrorists.”

“Blessed are those who kill them, as well as those whom they kill,” Sheikh Gomaa declared. The cameras caught Mr. Sisi listening attentively.

Using religion to legitimize the “coup leaders” and undermine their opponents has become extensive, said Emad Shahin, a respected political scientist who left Egypt because the new government charged him with conspiring against it.

But the complaints about continued sectarianism have not deterred church leaders from firmly supporting Mr. Sisi as their protector against worse treatment by the Muslim majority.

Over Easter weekend, Mr. Sisi made a private visit to the pope at the main cathedral but, unlike a rival presidential candidate, declined to attend Mass. The Mass nonetheless erupted into prolonged applause at the mention of Mr. Sisi’s name, state news media reported.